MND MERFISH Report
1. Overview
- Project: Human MND MERFISH Analysis
1.1 Sample Information
A brief sample information is generated from the submission table for the following analysis.
| Expt | Sample | Index | Genotype | Diagnosis | Block | RIN | Region | DataPath | Comment |
|---|---|---|---|---|---|---|---|---|---|
| 1 | H250 | H250 | Control | Control | M2 | 8.0 | region_0 | Y:/Lab/MERFISH_Imaging_data_2/202407221453_20240722Maize28H250BP1738h271x01_VMSC00101 | NA |
| 1 | MN28 | MN28 | MN | MNS-ALS/MidAD | M2 | 8.5 | region_1 | Y:/Lab/MERFISH_Imaging_data_2/202407221453_20240722Maize28H250BP1738h271x01_VMSC00101 | NA |
| 2 | H260 | H260 | Control | Control | M2 | 8.3 | region_0 | Y:/Lab/MERFISH_Imaging_data_2/202407221100_20240722105620240722Maize13H260xBP1738x2_VMSC05201 | NA |
| 2 | MN13 | MN13 | MN | MND-ALS | SM2 | 6.6 | region_1 | Y:/Lab/MERFISH_Imaging_data_2/202407221100_20240722105620240722Maize13H260xBP1738x2_VMSC05201 | Low Cell Detection |
| 3 | H264 | H264 | Control | Control | M2 | 8.2 | region_0 | Y:/Lab/MERFISH_Imaging_data_2/202407261252_20240726MaizeMN32H264BP1738x03_VMSC00101 | NA |
| 3 | MN32 | MN32 | MN | MND | M2 | 8.3 | region_1 | Y:/Lab/MERFISH_Imaging_data_2/202407261252_20240726MaizeMN32H264BP1738x03_VMSC00101 | NA |
| 4 | H262 | H262 | Control | Control/earlyAD | M2 | 4.3 | region_0 | Y:/Lab/MERFISH_Imaging_data_2/202408051335_20240805MaizeMN40H262BP1738x05_VMSC00101 | Low Cell Detection |
| 4 | MN40 | MN40 | MN | MND/AD | M2 | 7.8 | region_1 | Y:/Lab/MERFISH_Imaging_data_2/202408051335_20240805MaizeMN40H262BP1738x05_VMSC00101 | NA |
| 5 | H250 | H250_dup | Control | Control | M2 | 8.0 | region_0 | Y:/Lab/MERFISH_Imaging_data_2/202409091144_20240909MaizeMN28H250BP1738m271x04_VMSC00101 | NA |
| 5 | MN28 | MN28_dup | MN | MNS-ALS/MidAD | M2 | 8.5 | region_1 | Y:/Lab/MERFISH_Imaging_data_2/202409091144_20240909MaizeMN28H250BP1738m271x04_VMSC00101 | NA |
| 6 | H246 | H246 | Control | Control | M3 | 7.4 | region_0 | Y:/Lab/MERFISH_Imaging_data_2/202407261255_20240726MaizeMN31H246BP1738x04_VMSC05201 | Bad transcript quality! |
| 6 | MN31 | MN31 | MN | MND-ALS | M2 | 9.0 | region_1 | Y:/Lab/MERFISH_Imaging_data_2/202407261255_20240726MaizeMN31H246BP1738x04_VMSC05201 | Bad transcript quality! |
1.2 Submission Form
Sample Submission Form
2. Data Quality Control
2.1 MERSCOPE Quality Summary
The summaries present the data quality assessment automatically generated by MERSCOPE for each experiment. We mainly focus on the transcripts level for each sample. So we’re looking for high density in transcripts, based on the transcripts count per field of view (FOV), transcript density in FOV, and frequency of transcripts detected.
Generally, log10 transcript count > 4.0 in most area can be considered as a good quality standard.
Need to note that the low accuracy in DAPI cell boundary is not a concern, as a self-designed cell segmentation processing will take over this task.